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School:Chemistry
Chemistry (from Egyptian kēme (chem), meaning "earth") is the science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions. It is a physical science for studies of various atoms, molecules, crystals and other aggregates of matter whether in isolation or combination, which incorporates the concepts of energy and entropy in relation to the spontaneity of chemical processes. Modern chemistry evolved out of alchemy following the chemical revolution (1773). Disciplines within chemistry are traditionally grouped by the type of matter being studied or the kind of study. These include inorganic chemistry, the study of inorganic matter; organic chemistry, the study of organic matter; biochemistry, the study of substances found in biological organisms; physical chemistry, the energy related studies of chemical systems at macro, molecular and submolecular scales; analytical chemistry, the analysis of material samples to gain an understanding of their chemical composition and structure. Many more specialized disciplines have emerged in recent years, e.g. neurochemistry the chemical study of the nervous system (see subdisciplines). Summary Chemistry is the scientific study of interaction of chemical substances that are constituted of atoms or the subatomic particles: protons, electrons and neutrons.4 Atoms combine to produce molecules or crystals. Chemistry is often called "the central science" because it connects the other natural sciences such as astronomy, physics, material science, biology, and geology. The genesis of chemistry can be traced to certain practices, known as alchemy, which had been practiced for several millennia in various parts of the world, particularly the Middle East. The structure of objects we commonly use and the properties of the matter we commonly interact with, are a consequence of the properties of chemical substances and their interactions. For example, steel is harder than iron because its atoms are bound together in a more rigid crystalline lattice; wood burns or undergoes rapid oxidation because it can react spontaneously with oxygen in a chemical reaction above a certain temperature; sugar and salt dissolve in water because their molecular/ionic properties are such that dissolution is preferred under the ambient conditions. The transformations that are studied in chemistry are a result of interaction either between different chemical substances or between matter and energy. Traditional chemistry involves study of interactions between substances in a chemistry laboratory using various forms of laboratory glassware. Laboratory, Institute of Biochemistry, University of Cologne A chemical reaction is a transformation of some substances into one or more other substances. It can be symbolically depicted through a chemical equation. The number of atoms on the left and the right in the equation for a chemical transformation is most often equal. The nature of chemical reactions a substance may undergo and the energy changes that may accompany it are constrained by certain basic rules, known as chemical laws. Energy and entropy considerations are invariably important in almost all chemical studies. Chemical substances are classified in terms of their structure, phase as well as their chemical compositions. They can be analysed using the tools of chemical analysis, e.g. spectroscopy and chromatography. Chemistry is an integral part of the science curriculum both at the high school as well as the early college level. At these levels, it is often called "general chemistry" which is an introduction to a wide variety of fundamental concepts that enable the student to acquire tools and skills useful at the advanced levels, whereby chemistry is invariably studied in any of its various sub-disciplines. Scientists, engaged in chemical research are known as chemists. Most chemists specialize in one or more sub-disciplines. Basic concepts Several concepts are essential for the study of chemistry; some of them are: Atom Main article: Atom An atom is the basic unit of chemistry. It consists of a positively charged core (the atomic nucleus) which contains protons and neutrons, and which maintains a number of electrons to balance the positive charge in the nucleus. The atom is also the smallest entity that can be envisaged to retain some of the chemical properties of the element, such as electronegativity, ionization potential, preferred oxidation state(s), coordination number, and preferred types of bonds to form (e.g., metallic, ionic, covalent). Element Main article: Chemical element The concept of chemical element is related to that of chemical substance. A chemical element is characterized by a particular number of protons in the nuclei of its atoms. This number is known as the atomic number of the element. For example, all atoms with 6 protons in their nuclei are atoms of the chemical element carbon, and all atoms with 92 protons in their nuclei are atoms of the element uranium. However, several isotopes of an element, that differ from one another in the number of neutrons present in the nucleus, may exist. The most convenient presentation of the chemical elements is in the periodic table of the chemical elements, which groups elements by atomic number. Due to its ingenious arrangement, groups, or columns, and periods, or rows, of elements in the table either share several chemical properties, or follow a certain trend in characteristics such as atomic radius, electronegativity, etc. Lists of the elements by name, by symbol, and by atomic number are also available. Compound Main article: Chemical compound A compound is a substance with a particular ratio of atoms of particular chemical elements which determines its composition, and a particular organization which determines chemical properties. For example, water is a compound containing hydrogen and oxygen in the ratio of two to one, with the oxygen atom between the two hydrogen atoms, and an angle of 104.5° between them. Compounds are formed and interconverted by chemical reactions. Substance Main article: Chemical substance A chemical substance is a kind of matter with a definite composition and set of properties.33 Strictly speaking, a mixture of compounds, elements or compounds and elements is not a chemical substance, but it may be called a chemical. Most of the substances we encounter in our daily life are some kind of mixture; for example: air, alloys, biomass, etc. Nomenclature of substances is a critical part of the language of chemistry. Generally it refers to a system for naming chemical compounds. Earlier in the history of chemistry substances were given name by their discoverer, which often led to some confusion and difficulty. However, today the IUPAC system of chemical nomenclature allows chemists to specify by name specific compounds amongst the infinite variety of possible chemicals. The standard nomenclature of chemical substances is set by the International Union of Pure and Applied Chemistry (IUPAC). There are well-defined systems in place for naming chemical species. Organic compounds are named according to the organic nomenclature system.34 Inorganic compounds are named according to the inorganic nomenclature system.35 In addition the Chemical Abstracts Service has devised a method to index chemical substance. In this scheme each chemical substance is identifiable by a numeric number known as CAS registry number. Molecule Main article: Molecule A molecule is the smallest indivisible portion, besides an atom, of a pure chemical substance that has its unique set of chemical properties, that is, its potential to undergo a certain set of chemical reactions with other substances. Molecules can exist as electrically neutral units unlike ions. Molecules are typically a set of atoms bound together by covalent bonds, such that the structure is electrically neutral and all valence electrons are paired with other electrons either in bonds or in lone pairs. A molecular structure depicts the bonds and relative positions of atoms in a molecule such as that in Paclitaxel shown here One of the main characteristic of a molecule is its geometry often called its structure. While the structure of diatomic, triatomic or tetra atomic molecules may be trivial, (linear, angular pyramidal etc.) the structure of polyatomic molecules, that are constituted of more than six atoms (of several elements) can be crucial for its chemical nature. Mole Main article: Mole (unit) A mole is the amount of a substance that contains as many elementary entities (atoms, molecules or ions) as there are atoms in 0.012 kilogram (or 12 grams) of carbon-12, where the carbon-12 atoms are unbound, at rest and in their ground state.36 This number is known as the Avogadro constant, and is determined empirically. The currently accepted value is 6.02214179(30) × 1023 mol-1 (2007 CODATA). The best way to understand the meaning of the term "mole" is to compare it to terms such as dozen. Just as one dozen is equal to 12, one mole is equal to 6.02214179(30) × 1023. The term is used because it is much easier to say, for example, 1 mole of carbon atoms, than it is to say 6.02214179(30) × 1023 carbon atoms. Likewise, we can describe the number of entities as a multiple or fraction of 1 mole, e.g. 2 mole or 0.5 moles. Mole is an absolute number (having no units) and can describe any type of elementary object, although the mole's use is usually limited to measurement of subatomic, atomic, and molecular structures. The number of moles of a substance in one liter of a solution is known as its molarity. Molarity is the common unit used to express the concentration of a solution in physical chemistry. Ions and salts Main article: Ion An ion is a charged species, an atom or a molecule, that has lost or gained one or more electrons. Positively charged cations (e.g. sodium cation Na+) and negatively charged anions (e.g. chloride Cl−) can form a crystalline lattice of neutral salts (e.g. sodium chloride NaCl). Examples of polyatomic ions that do not split up during acid-base reactions are hydroxide (OH−) and phosphate (PO43−). Ions in the gaseous phase is often known as plasma. Acidity and base balance Main article: Acid A substance can often be classified as an acid or a base. This is often done on the basis of a particular kind of reaction, namely the exchange of protons between chemical compounds. However, an extension to this mode of classification was brewed up by the American chemist, Gilbert Newton Lewis; in this mode of classification the reaction is not limited to those occurring in an aqueous solution, thus is no longer limited to solutions in water. According to concept as per Lewis, the crucial things being exchanged are charges. There are several other ways in which a substance may be classified as an acid or a base, as is evident in the history of this concept. The acidity or base of a substance is defined most typically by the pH or "Power of Hydrogen" value. Hydrogen ions are the basis of pH values. Solutions with a pH equal to "7" are said to be neutral, those with pH values less than "7" are defined as acidic and those greater than "7" as being basic. Every solution such as water, salt, urine, and blood have different pH values. A human beings normal blood pH is between 7.35 – 7.45 (Slightly Alkaline) and a neutral pH range is 6.8 - 7.0. Normally, blood pH is maintained in this range by these two organs: *Lungs **Carbon dioxide (CO2) = “respiratory acid” **Only acid exhaled from the lungs *Kidneys **All other acids = “metabolic acids” **Broken down and excreted through urine What is “acidosis”? Acidosis is an increased acidity (i.e. an increased hydrogen ion concentration). If not further qualified, it usually refers to acidity of the blood plasma. Acidosis is said to occur when arterial pH falls below 7.35, while its counterpart (alkalosis) occurs at a pH over 7.45. Arterial blood gas analysis and other tests are required to separate the main causes. The term acidemia describes the state of low blood pH, while acidosis is used to describe the processes leading to these states. Nevertheless, physicians sometimes use the terms interchangeably. The distinction may be relevant where a patient has factors causing both acidosis and alkalosis, where the relative severity of both determines whether the result is a high or a low pH. The rate of cellular metabolic activity affects and, at the same time, is affected by the pH of the body fluids. In mammals, the normal pH of arterial blood lies between 7.35 and 7.50 depending on the species (e.g. healthy human-arterial blood pH varies between 7.35 and 7.45). Blood pH values compatible with life in mammals are limited to a pH range between 6.8 and 7.8. Changes in the pH of arterial blood (and therefore the extracellular fluid) outside this range result in irreversible cell damage. Acidosis can be detected using a device called an arterial Blood Gas Analyzer. * Respiratory acidosis Main article: Lungs Respiratory acidosis results from a build-up of carbon dioxide in the blood (hypercapnia) due to hypoventilation. It is most often caused by pulmonary problems, although head injuries, drugs (especially anaesthetics and sedatives), and brain tumors can cause this acidemia. Pneumothorax, emphysema, chronic bronchitis, asthma, severe pneumonia, and aspiration are among the most frequent causes. It can also occur as a compensatory response to chronic metabolic alkalosis. One key to distinguish between respiratory and metabolic acidosis is that in respiratory acidosis, the CO2 (triggered by the lungs) is increased while the bicarbonate is either normal (uncompensated) or increased (compensated). Compensation occurs if respiratory acidosis is present, and a chronic phase is entered with partial buffering of the acidosis through renal bicarbonate retention. However, in cases where chronic illnesses which compromise pulmonary function persist, such as late-stage emphysema and certain types of muscular dystrophy, compensatory mechanisms will be unable to reverse this acidotic condition. As metabolic bicarbonate production becomes exhausted, and extraeneous bicarbonate infusion can no longer reverse the extreme buildup of carbon dioxide associated with uncompensated respiratory acidosis, mechanical ventilation will usually be applied. * Metabolic acidosis Main article: Kidneys Metabolic acidosis is an increased production of metabolic acids, usually resulting from disturbances in the ability to excrete acid via the kidneys. Renal acidosis is associated with an accumulation of urea and creatinine as well as metabolic acid residues of protein catabolism. An increase in the production of other acids may also produce metabolic acidosis. For example, lactic acidosis may occur from 1) severe (PaO2 <36mm Hg) hypoxemia causing a fall in the rate of oxygen diffusion from arterial blood to tissues, or 2) hypoperfusion (e.g. hypovolemic shock) causing an inadequate blood delivery of oxygen to tissues. A rise in lactate out of proportion to the level of pyruvate, e.g. in mixed venous blood, is termed "excess lactate", and may also be an indicator of fermention due to anaerobic metabolism occurring in muscle cells, as seen during strenuous exercise. Once oxygenation is restored, the acidosis clears quickly. Another example of increased production of acids occurs in starvation and diabetic acidosis. It is due to the accumulation of ketoacids (ketosis) and reflects a severe shift from glycolysis to lipolysis for energy needs. Acid consumption from poisoning, elevated levels of iron in the blood, and chronically decreased production of bicarbonate may also produce metabolic acidosis. Metabolic acidosis is compensated for in the lungs, as increased exhalation of carbon dioxide promptly shifts the buffering equation to reduce metabolic acid. This is a result of stimulation to chemoreceptors which increases alveolar ventilation, leading to respiratory compensation, otherwise known as Kussmaul breathing (a specific type of hyperventilation). Should this situation persist the patient is at risk for exhaustion leading to respiratory failure. Mutations to the V-ATPase 'a4' or 'B1' isoforms result in distal renal tubular acidosis, a condition that leads to metabolic acidosis, in some cases with sensorineural deafness. Arterial blood gases will indicate low pH, low blood HCO3, and normal or low PaCO2. In addition to arterial blood gas, an anion gap can also differentiate between possible causes. The Henderson-Hasselbalch equation is useful for calculating blood pH, because blood is a buffer solution. The amount of metabolic acid accumulating can also be quantitated by using buffer base deviation, a derivative estimate of the metabolic as opposed to the respiratory component. In hypovolemic shock for example, approximately 50% of the metabolic acid accumulation is lactic acid, which disappears as blood flow and oxygen debt are corrected. Treatment of uncompensated metabolic acidosis is focused upon correcting the underlying problem. When metabolic acidosis is severe and can no longer be compensated for adequately by the lungs, neutralizing the acidosis with infusions of bicarbonate may be required. Phase Main article: Phase (matter) In addition to the specific chemical properties that distinguish different chemical classifications chemicals can exist in several phases. For the most part, the chemical classifications are independent of these bulk phase classifications; however, some more exotic phases are incompatible with certain chemical properties. A phase is a set of states of a chemical system that have similar bulk structural properties, over a range of conditions, such as pressure or temperature. Physical properties, such as density and refractive index tend to fall within values characteristic of the phase. The phase of matter is defined by the phase transition, which is when energy put into or taken out of the system goes into rearranging the structure of the system, instead of changing the bulk conditions. Sometimes the distinction between phases can be continuous instead of having a discrete boundary, in this case the matter is considered to be in a supercritical state. When three states meet based on the conditions, it is known as a triple point and since this is invariant, it is a convenient way to define a set of conditions. The most familiar examples of phases are solids, liquids, and gases. Many substances exhibit multiple solid phases. For example, there are three phases of solid iron (alpha, gamma, and delta) that vary based on temperature and pressure. A principal difference between solid phases is the crystal structure, or arrangement, of the atoms. Less familiar phases include plasmas, Bose-Einstein condensates and fermionic condensates and the paramagnetic and ferromagnetic phases of magnetic materials. While most familiar phases deal with three-dimensional systems, it is also possible to define analogs in two-dimensional systems, which has received attention for its relevance to systems in biology. Redox Main article: Redox It is a concept related to the ability of atoms of various substances to lose or gain electrons. Substances that have the ability to oxidize other substances are said to be oxidative and are known as oxidizing agents, oxidants or oxidizers. An oxidant removes electrons from another substance. Similarly, substances that have the ability to reduce other substances are said to be reductive and are known as reducing agents, reductants, or reducers. A reductant transfers electrons to another substance, and is thus oxidized itself. And because it "donates" electrons it is also called an electron donor. Oxidation and reduction properly refer to a change in oxidation number—the actual transfer of electrons may never occur. Thus, oxidation is better defined as an increase in oxidation number, and reduction as a decrease in oxidation number. Chemical bond Main article: Chemical bond Electron atomic and molecular orbitals A chemical bond is a concept for understanding how atoms stick together in molecules. It may be visualized as the multipole balance between the positive charges in the nuclei and the negative charges oscillating about them.39 More than simple attraction and repulsion, the energies and distributions characterize the availability of an electron to bond to another atom. These potentials create the interactions which hold atoms together in molecules or crystals. In many simple compounds, Valence Bond Theory, the Valence Shell Electron Pair Repulsion model (VSEPR), and the concept of oxidation number can be used to predict molecular structure and composition. Similarly, theories from classical physics can be used to predict many ionic structures. With more complicated compounds, such as metal complexes, valence bond theory fails and alternative approaches, primarily based on principles of quantum chemistry such as the molecular orbital theory, are necessary. See diagram on electronic orbitals. Chemical reaction Main article: Chemical reaction Chemical reaction is a concept related to the transformation of a chemical substance through its interaction with another, or as a result of its interaction with some form of energy. A chemical reaction may occur naturally or carried out in a laboratory by chemists in specially designed vessels which are often laboratory glassware. It can result in the formation or dissociation of molecules, that is, molecules breaking apart to form two or more smaller molecules, or rearrangement of atoms within or across molecules. Chemical reactions usually involve the making or breaking of chemical bonds. Oxidation, reduction, dissociation, acid-base neutralization and molecular rearrangement are some of the commonly used kinds of chemical reactions. A chemical reaction can be symbolically depicted through a chemical equation. While in a non-nuclear chemical reaction the number and kind of atoms on both sides of the equation are equal, for a nuclear reaction this holds true only for the nuclear particles viz. protons and neutrons. The sequence of steps in which the reorganization of chemical bonds may be taking place in the course of a chemical reaction is called its mechanism. A chemical reaction can be envisioned to take place in a number of steps, each of which may have a different speed. Many reaction intermediates with variable stability can thus be envisaged during the course of a reaction. Reaction mechanisms are proposed to explain the kinetics and the relative product mix of a reaction. Many physical chemists specialize in exploring and proposing the mechanisms of various chemical reactions. Several empirical rules, like the Woodward-Hoffmann rules often come handy while proposing a mechanism for a chemical reaction. A stricter definition is that "a chemical reaction is a process that results in the interconversion of chemical species". Under this definition, a chemical reaction may be an elementary reaction or a stepwise reaction. An additional caveat is made, in that this definition includes cases where the interconversion of conformers is experimentally observable. Such detectable chemical reactions normally involve sets of molecular entities as indicated by this definition, but it is often conceptually convenient to use the term also for changes involving single molecular entities (i.e. 'microscopic chemical events'). Energy Main article: Energy In the context of chemistry, energy is an attribute of a substance as a consequence of its atomic, molecular or aggregate structure. Since a chemical transformation is accompanied by a change in one or more of these kinds of structure, it is invariably accompanied by an increase or decrease of energy of the substances involved. Some energy is transferred between the surroundings and the reactants of the reaction in the form of heat or light; thus the products of a reaction may have more or less energy than the reactants. A reaction is said to be exothermic if the final state is lower on the energy scale than the initial state; in the case of endothermic reactions the situation is otherwise. Chemical reactions are invariably not possible unless the reactants surmount an energy barrier known as the activation energy. The speed of a chemical reaction (at given temperature T) is related to the activation energy E, by the Boltzmann's population factor e − E / kT - that is the probability of molecule to have energy greater than or equal to E at the given temperature T. This exponential dependence of a reaction rate on temperature is known as the Arrhenius equation. The activation energy necessary for a chemical reaction can be in the form of heat, light, electricity or mechanical force in the form of ultrasound. A related concept free energy, which also incorporates entropy considerations, is a very useful means for predicting the feasibility of a reaction and determining the state of equilibrium of a chemical reaction, in chemical thermodynamics. A reaction is feasible only if the total change in the Gibbs free energy is negative, \Delta G \le 0 \,; if it is equal to zero the chemical reaction is said to be at equilibrium. There exist only limited possible states of energy for electrons, atoms and molecules. These are determined by the rules of quantum mechanics, which require quantization of energy of a bound system. The atoms/molecules in a higher energy state are said to be excited. The molecules/atoms of substance in an excited energy state are often much more reactive; that is, more amenable to chemical reactions. The phase of a substance is invariably determined by its energy and the energy of its surroundings. When the intermolecular forces of a substance are such that the energy of the surroundings is not sufficient to overcome them, it occurs in a more ordered phase like liquid or solid as is the case with water (H2O); a liquid at room temperature because its molecules are bound by hydrogen bonds.43 Whereas hydrogen sulfide (H2S) is a gas at room temperature and standard pressure, as its molecules are bound by weaker dipole-dipole interactions. The transfer of energy from one chemical substance to another depends on the size of energy quanta emitted from one substance. However, heat energy is often transferred more easily from almost any substance to another because the phonons responsible for vibrational and rotational energy levels in a substance have much less energy than photons invoked for the electronic energy transfer. Thus, because vibrational and rotational energy levels are more closely spaced than electronic energy levels, heat is more easily transferred between substances relative to light or other forms of electronic energy. For example, ultraviolet electromagnetic radiation is not transferred with as much efficacy from one substance to another as thermal or electrical energy. The existence of characteristic energy levels for different chemical substances is useful for their identification by the analysis of spectral lines. Different kinds of spectra are often used in chemical spectroscopy, e.g. IR, microwave, NMR, ESR, etc. Spectroscopy is also used to identify the composition of remote objects - like stars and distant galaxies - by analyzing their radiation spectra. Chemical laws Main article: Chemical law Chemical reactions are governed by certain laws, which have become fundamental concepts in chemistry. Some of them are: * Avogadro's law * Beer-Lambert law * Boyle's law (1662, relating pressure and volume) * Charles's law (1787, relating volume and temperature) * Fick's law of diffusion * Gay-Lussac's law (1809, relating pressure and temperature) * Henry's law * Hess's Law * Law of conservation of energy leads to the important concepts of equilibrium, thermodynamics, and kinetics. * Law of conservation of mass, according to the modern physics it is actually energy that is conserved, and that energy and mass are related; a concept which becomes important in nuclear chemistry. * Law of definite composition, although in many systems (notably biomacromolecules and minerals) the ratios tend to require large numbers, and are frequently represented as a fraction. * Law of multiple proportions * Raoult's Law Further reading * Wikibooks: General Chemistry Category:Biomedical Engineering Technology